PDE Petrinet models

[danbryce]

This directory includes subdirectories (noted below) for multiple PDE problems that are encoded as Petri nets.

• halfar: ice dome model
• advection: advection model for incompressible flows

The files in each subdirectory use the naming scheme, as follows:

{problem}_{derivative}_{dimensions}_{boundary_slope}_{num_disc}.json

where

• problem: the name of the problem (e.g., advection)
• derivative: the method used to compute spatial derivatives (e.g., forward, backward, and centered)
• dimensions: the number of spatial dimensions (1, 2, or 3)
• boundary_slope: the coefficient for boundary conditions, expressed as u(x, t) = kt, where k = boundary_slope, t is the time (relative to starting time at 0), u is a state variable, and x is a boundary position.
• num_disc: the number of discrete points in each dimension (e.g., if dimension = 2 and num_disc = 5, then there will be 5^2 = 25 positions, not including boundaries).

The generator for these instances is currently available here, and a notebook illustrating the results of FUNMAN analyzing the models is available here.

---

Authored by dbryce@sift.net and dmosaphir@sift.net

[djinnome]

Hi @danbryce

I ran python model_inventory.py --format md ../petrinet/examples/pde/halfar/*.json in the validation directory, and there were no issues reported. Yay! :-)

However, when I ran python model_inventory.py --format md ../petrinet/examples/pde/advection/*.json I got the following results below. It appears that there are quite a few AMRs that do not have rate laws for all edges of the Petri net. Boo! :-(

source	parameter distribution exists	parameter dist/value set	rate laws present	rate law vars defined	initial values present	observables found
...ection_backward_1_0.01_10.json	True	True	True	True	True	0
...vection_backward_1_0.01_3.json	True	True	True	True	True	0
...vection_backward_1_0.01_5.json	True	True	True	True	True	0
...vection_backward_1_0.0_10.json	True	True	True	True	True	0
...dvection_backward_1_0.0_3.json	True	True	True	True	True	0
...dvection_backward_1_0.0_5.json	True	True	True	True	True	0
...vection_backward_1_0.1_10.json	True	True	True	True	True	0
...dvection_backward_1_0.1_3.json	True	True	True	True	True	0
...dvection_backward_1_0.1_5.json	True	True	True	True	True	0
...vection_backward_1_0.2_10.json	True	True	True	True	True	0
...dvection_backward_1_0.2_3.json	True	True	True	True	True	0
...dvection_backward_1_0.2_5.json	True	True	True	True	True	0
...ection_backward_2_0.01_10.json	True	True	True	True	True	0
...vection_backward_2_0.01_3.json	True	True	True	True	True	0
...vection_backward_2_0.01_5.json	True	True	True	True	True	0
...vection_backward_2_0.0_10.json	True	True	True	True	True	0
...dvection_backward_2_0.0_3.json	True	True	True	True	True	0
...dvection_backward_2_0.0_5.json	True	True	True	True	True	0
...vection_backward_2_0.1_10.json	True	True	True	True	True	0
...dvection_backward_2_0.1_3.json	True	True	True	True	True	0
...dvection_backward_2_0.1_5.json	True	True	True	True	True	0
...vection_backward_2_0.2_10.json	True	True	True	True	True	0
...dvection_backward_2_0.2_3.json	True	True	True	True	True	0
...dvection_backward_2_0.2_5.json	True	True	True	True	True	0
...ection_backward_3_0.01_10.json	True	True	True	True	True	0
...vection_backward_3_0.01_3.json	True	True	True	True	True	0
...vection_backward_3_0.01_5.json	True	True	True	True	True	0
...vection_backward_3_0.0_10.json	True	True	True	True	True	0
...dvection_backward_3_0.0_3.json	True	True	True	True	True	0
...dvection_backward_3_0.0_5.json	True	True	True	True	True	0
...vection_backward_3_0.1_10.json	True	True	True	True	True	0
...dvection_backward_3_0.1_3.json	True	True	True	True	True	0
...dvection_backward_3_0.1_5.json	True	True	True	True	True	0
...vection_backward_3_0.2_10.json	True	True	True	True	True	0
...dvection_backward_3_0.2_3.json	True	True	True	True	True	0
...dvection_backward_3_0.2_5.json	True	True	True	True	True	0
...ection_centered_1_0.01_10.json	True	True	True	False	True	0
...vection_centered_1_0.01_3.json	True	True	True	False	True	0
...vection_centered_1_0.01_5.json	True	True	True	False	True	0
...vection_centered_1_0.0_10.json	True	True	True	True	True	0
...dvection_centered_1_0.0_3.json	True	True	True	True	True	0
...dvection_centered_1_0.0_5.json	True	True	True	True	True	0
...vection_centered_1_0.1_10.json	True	True	True	False	True	0
...dvection_centered_1_0.1_3.json	True	True	True	False	True	0
...dvection_centered_1_0.1_5.json	True	True	True	False	True	0
...vection_centered_1_0.2_10.json	True	True	True	False	True	0
...dvection_centered_1_0.2_3.json	True	True	True	False	True	0
...dvection_centered_1_0.2_5.json	True	True	True	False	True	0
...ection_centered_2_0.01_10.json	True	True	True	False	True	0
...vection_centered_2_0.01_3.json	True	True	True	False	True	0
...vection_centered_2_0.01_5.json	True	True	True	False	True	0
...vection_centered_2_0.0_10.json	True	True	True	True	True	0
...dvection_centered_2_0.0_3.json	True	True	True	True	True	0
...dvection_centered_2_0.0_5.json	True	True	True	True	True	0
...vection_centered_2_0.1_10.json	True	True	True	False	True	0
...dvection_centered_2_0.1_3.json	True	True	True	False	True	0
...dvection_centered_2_0.1_5.json	True	True	True	False	True	0
...vection_centered_2_0.2_10.json	True	True	True	False	True	0
...dvection_centered_2_0.2_3.json	True	True	True	False	True	0
...dvection_centered_2_0.2_5.json	True	True	True	False	True	0
...ection_centered_3_0.01_10.json	True	True	True	False	True	0
...vection_centered_3_0.01_3.json	True	True	True	False	True	0
...vection_centered_3_0.01_5.json	True	True	True	False	True	0
...vection_centered_3_0.0_10.json	True	True	True	True	True	0
...dvection_centered_3_0.0_3.json	True	True	True	True	True	0
...dvection_centered_3_0.0_5.json	True	True	True	True	True	0
...vection_centered_3_0.1_10.json	True	True	True	False	True	0
...dvection_centered_3_0.1_3.json	True	True	True	False	True	0
...dvection_centered_3_0.1_5.json	True	True	True	False	True	0
...vection_centered_3_0.2_10.json	True	True	True	False	True	0
...dvection_centered_3_0.2_3.json	True	True	True	False	True	0
...dvection_centered_3_0.2_5.json	True	True	True	False	True	0
...vection_forward_1_0.01_10.json	True	True	True	False	True	0
...dvection_forward_1_0.01_3.json	True	True	True	False	True	0
...dvection_forward_1_0.01_5.json	True	True	True	False	True	0
...dvection_forward_1_0.0_10.json	True	True	True	True	True	0
...advection_forward_1_0.0_3.json	True	True	True	True	True	0
...advection_forward_1_0.0_5.json	True	True	True	True	True	0
...dvection_forward_1_0.1_10.json	True	True	True	False	True	0
...advection_forward_1_0.1_3.json	True	True	True	False	True	0
...advection_forward_1_0.1_5.json	True	True	True	False	True	0
...dvection_forward_1_0.2_10.json	True	True	True	False	True	0
...advection_forward_1_0.2_3.json	True	True	True	False	True	0
...advection_forward_1_0.2_5.json	True	True	True	False	True	0
...vection_forward_2_0.01_10.json	True	True	True	False	True	0
...dvection_forward_2_0.01_3.json	True	True	True	False	True	0
...dvection_forward_2_0.01_5.json	True	True	True	False	True	0
...dvection_forward_2_0.0_10.json	True	True	True	True	True	0
...advection_forward_2_0.0_3.json	True	True	True	True	True	0
...advection_forward_2_0.0_5.json	True	True	True	True	True	0
...dvection_forward_2_0.1_10.json	True	True	True	False	True	0
...advection_forward_2_0.1_3.json	True	True	True	False	True	0
...advection_forward_2_0.1_5.json	True	True	True	False	True	0
...dvection_forward_2_0.2_10.json	True	True	True	False	True	0
...advection_forward_2_0.2_3.json	True	True	True	False	True	0
...advection_forward_2_0.2_5.json	True	True	True	False	True	0
...vection_forward_3_0.01_10.json	True	True	True	False	True	0
...dvection_forward_3_0.01_3.json	True	True	True	False	True	0
...dvection_forward_3_0.01_5.json	True	True	True	False	True	0
...dvection_forward_3_0.0_10.json	True	True	True	True	True	0
...advection_forward_3_0.0_3.json	True	True	True	True	True	0
...advection_forward_3_0.0_5.json	True	True	True	True	True	0
...dvection_forward_3_0.1_10.json	True	True	True	False	True	0
...advection_forward_3_0.1_3.json	True	True	True	False	True	0
...advection_forward_3_0.1_5.json	True	True	True	False	True	0
...dvection_forward_3_0.2_10.json	True	True	True	False	True	0
...advection_forward_3_0.2_3.json	True	True	True	False	True	0
...advection_forward_3_0.2_5.json	True	True	True	False	True	0